To my mind, stripping is not ignoring ;-), but I understand what you mean, sphinx ignores as it pays attention and strips.

[2] is the commit for [1], and both are from 3 years ago, long before 3.2.0. Does the true-by-default ``trim_doctest_flags`` config value work on a file by file basis, so that it can just be added to doctest.rst?

I have no opinion of sphinx versions, which I am ignorant about. I just know that the mistaken stripping destroys the value of the examples, making the result very confusing.